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Automated sequence design of 2D wireframe DNA origami with honeycomb edges

Author

Listed:
  • Hyungmin Jun

    (Massachusetts Institute of Technology)

  • Xiao Wang

    (Massachusetts Institute of Technology)

  • William P. Bricker

    (Massachusetts Institute of Technology)

  • Mark Bathe

    (Massachusetts Institute of Technology)

Abstract

Wireframe DNA origami has emerged as a powerful approach to fabricating nearly arbitrary 2D and 3D geometries at the nanometer-scale. Complex scaffold and staple routing needed to design wireframe DNA origami objects, however, render fully automated, geometry-based sequence design approaches essential for their synthesis. And wireframe DNA origami structural fidelity can be limited by wireframe edges that are composed only of one or two duplexes. Here we introduce a fully automated computational approach that programs 2D wireframe origami assemblies using honeycomb edges composed of six parallel duplexes. These wireframe assemblies show enhanced structural fidelity from electron microscopy-based measurement of programmed angles compared with identical geometries programmed using dual-duplex edges. Molecular dynamics provides additional theoretical support for the enhanced structural fidelity observed. Application of our top-down sequence design procedure to a variety of complex objects demonstrates its broad utility for programmable 2D nanoscale materials.

Suggested Citation

  • Hyungmin Jun & Xiao Wang & William P. Bricker & Mark Bathe, 2019. "Automated sequence design of 2D wireframe DNA origami with honeycomb edges," Nature Communications, Nature, vol. 10(1), pages 1-9, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13457-y
    DOI: 10.1038/s41467-019-13457-y
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    Cited by:

    1. Jae Young Lee & Yanggyun Kim & Do-Nyun Kim, 2024. "Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    2. Molly F. Parsons & Matthew F. Allan & Shanshan Li & Tyson R. Shepherd & Sakul Ratanalert & Kaiming Zhang & Krista M. Pullen & Wah Chiu & Silvi Rouskin & Mark Bathe, 2023. "3D RNA-scaffolded wireframe origami," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    3. Jae Young Lee & Heeyuen Koh & Do-Nyun Kim, 2023. "A computational model for structural dynamics and reconfiguration of DNA assemblies," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    4. Chi Chen & Xingfei Wei & Molly F. Parsons & Jiajia Guo & James L. Banal & Yinong Zhao & Madelyn N. Scott & Gabriela S. Schlau-Cohen & Rigoberto Hernandez & Mark Bathe, 2022. "Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami," Nature Communications, Nature, vol. 13(1), pages 1-15, December.

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